Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__psRCH2:GFF3101 Length = 255 Score = 111 bits (277), Expect = 2e-29 Identities = 75/233 (32%), Positives = 126/233 (54%), Gaps = 16/233 (6%) Query: 4 SQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGD 63 S P+I+MQG+ K FG L +++ V GE L G +G+GKST I+ ++ + + +G Sbjct: 12 SGPVIQMQGVHKWFGQFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGR 71 Query: 64 ILFEGQPLHFADPR--DAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDH 121 I+ G L +D + +AI + + V QH + P ++V +N + +RK+ Sbjct: 72 IVINGVELT-SDLKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMWVRKL------PR 124 Query: 122 DYANRITMEEMRKMGINLRGPDQA---VGTLSGGERQTVAIARAVHFGAKVLILDEPTSA 178 A I M + ++ I P+QA G LSGG++Q VAIARA+ K+++ DEPTSA Sbjct: 125 RQAEEIAMHYLERVRI----PEQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSA 180 Query: 179 LGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQ 231 L VL T+ + + G+ ++ +TH + A V DR +++G+ + A+ Sbjct: 181 LDPEMVKEVLDTMVSLAESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAE 233 Lambda K H 0.321 0.137 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 152 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 261 Length of database: 255 Length adjustment: 24 Effective length of query: 237 Effective length of database: 231 Effective search space: 54747 Effective search space used: 54747 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory